Could you give the new command a different name? ALIGN is misleading since
you are not doing an alignment, but just a superposition.
http://en.wikipedia.org/wiki/Structural_alignment
Thanks,
Andreas
On Mon, Mar 15, 2010 at 6:05 AM, Robert Hanson <[email protected]> wrote:
> Kersten,
>
> I have had some success in aligning your RNA fragments. Please get back to
> me.
>
> Jmol 11.9.34 will align proteins, RNA, and DNA based on quaternion frames
> using a new ALIGN command.
>
> See files in
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/align
>
> for examples.
>
> This is a little different from what you are doing there at your site,
> though it is very close. Jmol is aligning the models to give the smallest
> standard deviation for a set of quaternions representing the orientations of
> the base pairs. As such, it does require prior knowledge of which bases are
> to be matched. So the alignment command I used was this:
>
> load files "t1.pdb" "t2.pdb"
> frame *
> color group
> set quaternionFrame "C"
> qset1 = quaternion({41-46/1.1}) + quaternion({27-31/2.1})
> qset2 = quaternion({77-82/2.1}) + quaternion({92-100/2.1})
> align {2.1} {1.1} @qset2 @qset1
>
> Where t1 and t2 are the starting files you have there for at
> http://www.dundee.ac.uk/biocentre/nasg/kturn/sites/U4kturnSite.html
>
> Let me explain what this is doing:
>
> First, both files are loaded.
>
> The quaternionFrame "C" setting tells Jmol you want to align based on
> nucleic acid bases. Another option is quaternionFrame "P", which aligns
> based on the orientations of the tetrahedral phosphorus. But the standard
> deviation was somewhat higher for that when I tried it.
>
> qset1 and qset2 are each sets of quaternions. I only have preliminary
> manuscripts on how these are set up, but the basic idea is that there is a
> little xyz axis set (a "quaternion frame") on each base. You can display
> those using:
>
> select *
> frame 1
> draw quaternions
> frame 2
> draw quaternions
> frame *
>
> Jmol is optimizing the relative orientation of these quaternion frames.
>
> I have to do the concatenation business because the ordering of atoms in
> the files are reversed for the two chains -- we need to match bases 77-82
> and 92-100 in aligned_to_Kt7/3CC2_HmKt7.pdb (t2.pdb) with bases 41-46 and
> 27-31 in aligned_to_Kt7/1E7K_U4kt.pdb (t1.pdb), respectively.
>
> I could have left that out and just done
>
> align {2.1} {1.1}
>
> if these had instead been in sequential order.
>
> The ALIGN command then aligns model 2 with model 1 by first finding the
> optimum rotation to align the bases based on these quaternion sets, then
> doing a simple center-of-geometry translation. It uses a very fast and
> robust but rather new method referred to as the determination of the
> "spherical mean" from:
>
> Samuel R. Buss, Jay P.
> Fillmore<http://www.informatik.uni-trier.de/%7Eley/db/indices/a-tree/f/Fillmore:Jay_P=.html>:
> Spherical averages and applications to spherical splines and interpolation.
> ACM
> Trans. Graph.
> 20<http://www.informatik.uni-trier.de/%7Eley/db/journals/tog/tog20.html#BussF01>(2):
> 95-126 (2001)
>
>
> Of course, whether or not this is an acceptable alignment is questionable.
> Certainly it has never been done this way before. Still, there are a lot of
> variables here, and I could imagine different ways of going about it. It's
> not necessarily as simple as "find the smallest root mean square deviation
> for the set of atoms" -- because of course we have purines and pyrimidines
> mixed along the chains. So perhaps this is an acceptable way to align the
> fragments. It's certainly very fast!
>
> I would argue that Jmol's ALIGN command has given a better alignment of the
> bases themselves; your alignment probably better matches exact atom
> positions. Only you can decide which is "better."
>
> Some questions:
>
> Q: How important is that Jmol produce EXACTLY the result you show at that
> site?
>
> Q: Do you have a reference to the algorithm that is being used by your
> software?
>
> Q: Would you like to work with me to make the ALIGN command work better for
> your purposes?
>
> The jar files needed for this analysis are for Jmol 11.9.34_dev, in
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>
> Hope to hear from you soon.
>
> Bob
>
>
> On Mon, Mar 8, 2010 at 9:43 AM, Kersten Schroeder <
> [email protected]> wrote:
>
>> Dear Robert,
>>
>> I really enjoy Jmol and am currently using it on a website I help create
>> for the kink-turn RNA motif (
>> http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_all.php).
>>
>> Do you plan to develop a way to align model 1 onto model 2 in Jmol script?
>> Pairfit in PyMol does it, so there may be a python code available to help
>> develop in Javascript. I want to align one model (of a list of 30) to
>> another model (of the same list of 30). Therefore, pre-aligning elsewhere
>> would need to be done about 900 times.
>>
>> I look forward to your input. Thank you and have a good day.
>>
>> Kersten Schroeder
>>
>> Kersten Schroeder, Ph.D.
>> MSI/WTB complex,
>> Dow Street,
>> University of Dundee,
>> Dundee DD1 5EH
>> UK
>>
>>
>>
>> ************************************************************
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>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
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